Molecular Dynamics Simulations in Aqueous Solution:  Application to Free Energy Calculation of Oligopeptides

1998 ◽  
Vol 102 (33) ◽  
pp. 6419-6424 ◽  
Author(s):  
Koichi Tazaki ◽  
Kentaro Shimizu
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Dynamics Simulations

scholarly journals Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

2014 ◽  
Vol 10 (7) ◽  
pp. 2677-2689 ◽  
Author(s):  
Yinglong Miao ◽  
William Sinko ◽  
Levi Pierce ◽  
Denis Bucher ◽  
Ross C. Walker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations

Insights into the effects of mutations on Cren7–DNA binding using molecular dynamics simulations and free energy calculations

2015 ◽  
Vol 17 (8) ◽  
pp. 5704-5711 ◽  
Author(s):  
Lin Chen ◽  
Qing-Chuan Zheng ◽  
Hong-Xing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Dynamic Effects ◽  
Cellular Processes ◽  
Dynamics Simulations

Cren7 is involved in regulating essential cellular processes. We applied MD simulations and free energy calculation to explore the structural and dynamic effects of W26A, L28A, and K53A mutations.

scholarly journals Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution fromAb InitioPotential and Molecular Dynamics Simulations

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
S. Tolosa ◽  
A. Hidalgo ◽  
J. A. Sansón
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Molecular Dynamics Simulations ◽  
Infinite Dilution ◽  
Theoretical Study ◽  
Water Model ◽  
Dynamics Simulations ◽  
Hydrolysis Of

A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described usingab initiosolute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3) via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

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